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INCF Digital Atlasing Infrastructure: An Overview

INCF Digital Atlasing Infrastructure: An Overview. Central role of WHS space. INCF DAI Architecture: WHS-aware APIs. WHS-aware Applications/Tools. WHS-aware Integration Resources. INCF WHS Ontology Server. INCF WHS Resource Registry. Internet. WHS API. WHS API. WHS API.

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INCF Digital Atlasing Infrastructure: An Overview

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  1. INCF Digital Atlasing Infrastructure:An Overview

  2. Central role of WHS space

  3. INCF DAI Architecture: WHS-aware APIs WHS-aware Applications/Tools WHS-aware Integration Resources INCF WHS Ontology Server INCF WHS Resource Registry Internet WHS API WHS API WHS API WHS API WHS API WHS API Atlas Resource … Atlas Resource Compute Resource … Compute Resource

  4. Managing multiple data types

  5. Client INCF-DAI: Path to Adoption + metadata Register to Atlas Query Visualize Analyze Servers & Databases Integration APIs Spatial Transformations Integrate Data Upload Semantic Integration Spatial Integration Database Integration Standards + metadata Image APIs Microarray APIs Imaging Spatial registry Microarray Information

  6. Demonstration

  7. Demo Contributors Neuroscience scenarios: Maryann Martone, Stephen Larson (UCSD), Jyl Boline (Informed Minds), Lydia Ng and Mike Hawrylycz (Allen Institute), Al Johnson (Duke University) WHS dataset: Al Johnson and Jeff Brandenburg (Duke University), Jonathan Nissanov and Pablo Burstein (Drexel University) Other datasets and meshes: Maryann Martone and Stephen Larson (UCSD), Lydia Ng and Chris Lau (Allen Institute) INCF Central and atlas service wrappers: Asif Memon (UCSD) INCF hubs and local services: Lydia Ng (Allen Institute), Albert Burger (MRC, UK), Kenneth McLeod (Heriot-Watt Univ, UK), Asif Memon (UCSD) Spatial transformations and anatomic structure lookup: Lydia Ng (Allen Institute), Steven Lamont and Alexander Young (UCSD) Representation of coordinate spaces: Alexander Young (UCSD) Client development: Stephen Larson and UCSD team; Seth Ruffins and UCLA team Hardware and server setup: Larry Lui (UCSD) Architecture: Albert, Fons, Jyl, Mike, Janis, Ilya Thanks to Jyl and Janis for coordination!

  8. Demo overview

  9. Atlas Services (As of August 2009; planned services in italic) Service = some functionality that you can call over the web in a standard manner

  10. INCF Central, and INCF Services and Hubs WHS Service ABA Service INCF Central: Service registry, Registry of spaces, Metadata catalog Other… UCSDService Other… EMAGEService

  11. Atlasing Infrastructure User Interface Present information about atlasing hubs Query atlasing hubs webservices webservices webservices INCF Spatial Server INCF Concept Server INCF Registry INCF DAI Infrastructure Components webservices webservices webservices ABA: INCF Hub EMAGE: INCF Hub UCSD: INCF Hub Harvest metadata from atlasinghubs Atlasing Hubs All components built on standards WHS canonical space and dataset Standard terminologies Standard services and exchange schemas

  12. Spatial transformations enable positioning a point of interest (POI) at approximately the same location in different atlases. (1.19,5.13,1.70) ABAvoxel to ABAreference (1.0,4.3,1.78) WHS to Paxinos to WHS AGEA,ABAvoxel (308,642,224) (AGEA:3825,5650,4650)

  13. Summary • We developed concepts of INCF-DAI, atlas hubs and services, INCF Central server, and communications between them • We built service-oriented architecture prototype for distributed digital atlases of mouse brain, that relies, where possible: • On standard service descriptions and exchange schemas • On standardized spaces, and a registry of spaces • On a collection of coordinate translation services, with WHS at the center • On standard terminology, with term cross-walks where needed • The translation services have performed well, and several tools were built for testing their performance • Data from several atlas hubs can be spatially integrated for the first time, via services and service chains • The integration has been demonstrated with a novel3D Atlas Integration application • The system is extensible

  14. Discussion

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